http://lod.bco-dmo.org/id/dataset/674398
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2017-01-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microbial orders comprising the core microbiome across all samples as measured by taxa prevalence, 2009-2012 (HERBVRE project)
2017-01-10
publication
2017-01-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-08-05
publication
https://doi.org/10.26008/1912/bco-dmo.674398.1
Deron Burkepile
Florida International University
principalInvestigator
Rebecca Vega Thurber
Florida International University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Burkepile, D., Vega Thurber, R. (2021) Microbial orders comprising the core microbiome across all samples as measured by taxa prevalence, 2009-2012 (HERBVRE project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-01-10 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.674398.1 [access date]
Core microbiome Dataset Description: <p>This dataset contains microbial orders comprising the core microbiome across all samples as measured by taxa prevalence, from Florida Keys National Marine Sanctuary.&nbsp;Cyanobacteria, Bacteroidetes and Actinobacteria were most abundant in all coral genera, with a core set of 13 bacterial orders in ≥95% of all samples. Published in&nbsp;&nbsp;Nature Communications (2016) doi:10.1038/ncomms11833, Supplementary Data 3a.</p>
<p><u>Natural history of the study site:&nbsp;</u><br />
This experiment was conducted in the area of Pickles Reef (24.99430, -80.40650), located east of Key Largo, Florida in the United States. The Florida Keys reef tract consists of a large bank reef system located approximately 8 km offshore of the Florida Keys, USA, and paralleling the island chain. Our study reef is a 5-6 m deep spur and groove reef system within this reef tract. The reefs of the Florida Keys have robust herbivorous fish populations and are relatively oligotrophic. Coral cover on most reefs in the Florida Keys, including our site, is 5-10%, while macroalgal cover averages ~15%, but ranges from 0-70% depending on location and season. Parrotfishes (<em>Scaridae</em>) and surgeonfishes (<em>Acanthuridae</em>) are the dominant herbivores on these reefs as fishing for them was banned in 1981. The other important herbivore on Caribbean reefs, the urchin <em>Diadema antillarum</em>, remains at low densities across the Florida Keys following the mass mortality event in 1982-3.</p>
<p><strong>Related Reference:</strong><br />
Zaneveld, J.R., D.E. Burkepile, A.A. Shantz, C. Pritchard, R. McMinds, J. Payet, R. Welsh, A.M.S. Correa, N.P. Lemoine, S. Rosales, C.E. Fuchs, and R. Vega Thurber (2016) Overfishing, nutrient pollution, and temperature interact to disrupt coral reefs down to microbial scales. Nature Communications 7:11833 <a href="http://www.nature.com/articles/ncomms11833" target="_blank">doi:10.1038/ncomms11833</a> <a href="http://www.nature.com/articles/ncomms11833#supplementary-information" target="_blank">Supplementary Information</a></p> Methods and Sampling: <p>To identify how algal communities and nutrient pollution affected the coral microbiome, we collected DNA samples from the surface mucus layer of 80 coral colonies (genera&nbsp;Porites, Siderastrea&nbsp;and&nbsp;Agaricia) at approximately monthly intervals. From these samples, 478 were used for 16S ribosomal RNA (rRNA) gene amplicon analyses following quality control (<a href="http://www.nature.com/articles/ncomms11833#s3" target="_blank">Supplementary Data 2 sheets a–d</a>). (Zaneveld, 2016)</p>
<p>Analysis of microbial β-diversity: Microbial community β-diversity was calculated based on the weighted UniFrac distance matrix67. This is a phylogenetic measure of community similarity that takes into account organismal abundance and phylogeny67. Phylogenetic trees used to calculate this metric were constructed in QIIME 1.8 (ref.&nbsp;65) through alignment of representative sequences of each OTU with PyNAST against the greengenes core set alignment66, and approximate maximum likelihood phylogenetic inference with FastTree. We considered the pool of distances between samples within each metadata category of interest (for example, algal competition or categories of temperature) using QIIME’s make_distance_boxplots.py. Significance was assessed by non-parametric&nbsp;t-tests, each with 1,000 Monte Carlo permutations (permutation is important in this instance to account for the non-independence of distances). The effect of this procedure is to ask whether different factors increase the dispersion of communities. PCoA plots of β-diversity were visualized in the Emperor software. When multiple categories (for example, different algal types) were tested for effects on β-diversity, the false discovery rate (FDR) for multiple comparisons was controlled at a threshold of&nbsp;q=0.05 using the Bejamini–Hochberg method. (Zaneveld, 2016)</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1130786 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1130786
completed
Deron Burkepile
Florida International University
805-893-3067
Department of Ecology, Evolution, and Marine Biology
Santa Barbara
CA
93106
USA
dburkepile@ucsb.edu
pointOfContact
Rebecca Vega Thurber
Florida International University
rvegathurber@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
taxonomy
all_tmt_95pcent
all_tmt_75pcent
all_tmt_50pcent
core_only_95pcent
core_only_75pcent
core_only_50pcent
theme
None, User defined
taxon
flag
featureType
BCO-DMO Standard Parameters
Burkepile_FL_Keys
service
Deployment Activity
Pickles Reef, east of Key Largo, FL
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Cascading interactions of herbivore loss and nutrient enrichment on coral reef macroalgae, corals, and microbial dynamics
https://osprey.bco-dmo.org/project/529590
Cascading interactions of herbivore loss and nutrient enrichment on coral reef macroalgae, corals, and microbial dynamics
<p><em>Description from NSF award abstract:</em><br />
Coral reefs in the Caribbean Sea are undergoing unprecedented declines in coral cover due in large part to climate change, pollution, and reductions in fish biodiversity and abundance. Macroalgae have become abundant on reefs, probably due to decreases in herbivory (e.g., through overfishing) and increases in anthropogenic inputs of nutrients. The spread of macroalgae has negative feedbacks on reef recovery because algae are often superior competitors and suppress growth of both adult and juvenile corals. A majority of reef studies to date have focused on how stressors affect macroorganisms, while relatively few have investigated how these stressors and the resultant algal-dominated states affect microorganisms. Yet, coral reef-associated microbes play significant roles in coral reef ecosystems through biogeochemical cycling and disease. Since microbes are important mutualists of corals as well as potential pathogens, it is important to understand the mechanisms that control their taxonomic and functional diversity.</p>
<p>The goal of this proposal is to quantify how alterations of top-down (removal of herbivorous fish) and bottom-up (inorganic nutrient addition) forces alter macrobial as well as microbial dynamics on coral reefs in order to understand the mechanisms that reinforce coral-depauperate reef systems. This work asks two main questions:</p>
<p>Q1. How do nutrient enrichment and herbivore removal interact to affect benthic algal abundance, coral-algal interactions, and coral survivorship and growth?</p>
<p>Q2. How do nutrient enrichment and herbivore removal affect bacterial abundance, taxonomic diversity, and functional diversity on and within corals?</p>
<p>The proposed research will directly and empirically address many of the current hypotheses about how bottom-up and top-down forces alter reef dynamics. The PIs will investigate: (1) the impact of multiple stressors over several years; (2) impacts on multiple levels of biological organization (from fishes to algae to microbes); and (3) the mechanisms underlying changes in algal-coral microbe interactions. Significantly, the approach will provide the statistical power necessary to distinguish between seasonal- and stress-induced changes in macro- and microbial diversity.</p>
<p><strong>Resulting Publication:</strong><br />
Zaneveld, J.R., D.E. Burkepile, A.A. Shantz, C. Pritchard, R. McMinds, J. Payet, R. Welsh, A.M.S. Correa, N.P. Lemoine, S. Rosales, C.E. Fuchs, and R. Vega Thurber (2016) Overfishing, nutrient pollution, and temperature interact to disrupt coral reefs down to microbial scales. Nature Communications 7:11833 doi:10.1038/ncomms11833.<br />
Access to data via <a href="http://www.nature.com/articles/ncomms11833#supplementary-information" target="_blank">Supplementary Information</a>.</p>
HERBVRE
largerWorkCitation
project
eng; USA
biota
oceans
Pickles Reef, east of Key Largo, FL
-80.4065
-80.4065
24.9943
24.9943
2017-01-10
Key Largo, Florida Keys, USA; N 24.99430, W 080.40650
0
BCO-DMO catalogue of parameters from Microbial orders comprising the core microbiome across all samples as measured by taxa prevalence, 2009-2012 (HERBVRE project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/674424.rdf
Name: taxonomy
Units: unitless
Description: <p>microbe taxonomic identification from QIIME Greengenes 13_8</p>
http://lod.bco-dmo.org/id/dataset-parameter/674425.rdf
Name: all_tmt_95pcent
Units: unitless
Description: <p>95% carriage of the microbial order in coral mucus samples across all treatments</p>
http://lod.bco-dmo.org/id/dataset-parameter/674426.rdf
Name: all_tmt_75pcent
Units: unitless
Description: <p>75% carriage of the microbial order in coral mucus samples across all treatments</p>
http://lod.bco-dmo.org/id/dataset-parameter/674427.rdf
Name: all_tmt_50pcent
Units: unitless
Description: <p>50% carriage of the microbial order in coral mucus samples across all treatments</p>
http://lod.bco-dmo.org/id/dataset-parameter/674428.rdf
Name: core_only_95pcent
Units: unitless
Description: <p>95% carriage of the microbial order in coral mucus samples for Greengenes core set only</p>
http://lod.bco-dmo.org/id/dataset-parameter/674429.rdf
Name: core_only_75pcent
Units: unitless
Description: <p>75% carriage of the microbial order in coral mucus samples for Greengenes core set only</p>
http://lod.bco-dmo.org/id/dataset-parameter/674430.rdf
Name: core_only_50pcent
Units: unitless
Description: <p>50% carriage of the microbial order in coral mucus samples for Greengenes core set only</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
4509
https://darchive.mblwhoilibrary.org/bitstream/1912/27415/1/dataset-674398_suppl-3a-core-microbiome__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.674398.1
download
onLine
dataset
<p>To identify how algal communities and nutrient pollution affected the coral microbiome, we collected DNA samples from the surface mucus layer of 80 coral colonies (genera&nbsp;Porites, Siderastrea&nbsp;and&nbsp;Agaricia) at approximately monthly intervals. From these samples, 478 were used for 16S ribosomal RNA (rRNA) gene amplicon analyses following quality control (<a href="http://www.nature.com/articles/ncomms11833#s3" target="_blank">Supplementary Data 2 sheets a–d</a>). (Zaneveld, 2016)</p>
<p>Analysis of microbial β-diversity: Microbial community β-diversity was calculated based on the weighted UniFrac distance matrix67. This is a phylogenetic measure of community similarity that takes into account organismal abundance and phylogeny67. Phylogenetic trees used to calculate this metric were constructed in QIIME 1.8 (ref.&nbsp;65) through alignment of representative sequences of each OTU with PyNAST against the greengenes core set alignment66, and approximate maximum likelihood phylogenetic inference with FastTree. We considered the pool of distances between samples within each metadata category of interest (for example, algal competition or categories of temperature) using QIIME’s make_distance_boxplots.py. Significance was assessed by non-parametric&nbsp;t-tests, each with 1,000 Monte Carlo permutations (permutation is important in this instance to account for the non-independence of distances). The effect of this procedure is to ask whether different factors increase the dispersion of communities. PCoA plots of β-diversity were visualized in the Emperor software. When multiple categories (for example, different algal types) were tested for effects on β-diversity, the false discovery rate (FDR) for multiple comparisons was controlled at a threshold of&nbsp;q=0.05 using the Bejamini–Hochberg method. (Zaneveld, 2016)</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date, reference information<br />
- renamed parameters to BCO-DMO standard</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Deployment: Burkepile_FL_Keys
Burkepile_FL_Keys
Florida Keys National Marine Sanctuary
shoreside
Florida Keys National Marine Sanctuary
shoreside